{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T14:48:57Z","timestamp":1778856537599,"version":"3.51.4"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,8,25]],"date-time":"2021-08-25T00:00:00Z","timestamp":1629849600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001665","name":"French National Research Agency","doi-asserted-by":"publisher","award":["ANR-19-PI3A-0004"],"award-info":[{"award-number":["ANR-19-PI3A-0004"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>MoMA-LoopSampler is a sampling method that globally explores the conformational space of flexible protein loops. It combines a large structural library of three-residue fragments and a novel reinforcement-learning-based approach to accelerate the sampling process while maintaining diversity. The method generates a set of statistically likely loop states satisfying geometric constraints, and its ability to sample experimentally observed conformations has been demonstrated. This paper presents a web user interface to MoMA-LoopSampler through the illustration of a typical use-case.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>MoMA-LoopSampler is freely available at: https:\/\/moma.laas.fr\/applications\/LoopSampler\/. We recommend users to create an account, but anonymous access is possible. In most cases, jobs are completed within a few minutes. The waiting time may increase depending on the server load, but it very rarely exceeds an hour. For users requiring more intensive use, binaries can be provided upon request.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab584","type":"journal-article","created":{"date-parts":[[2021,8,25]],"date-time":"2021-08-25T13:51:39Z","timestamp":1629899499000},"page":"552-553","source":"Crossref","is-referenced-by-count":13,"title":["MoMA-LoopSampler: a web server to exhaustively sample protein loop conformations"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5580-2842","authenticated-orcid":false,"given":"Am\u00e9lie","family":"Barozet","sequence":"first","affiliation":[{"name":"LAAS-CNRS, Universit\u00e9 de Toulouse, CNRS , F-31400 Toulouse, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kevin","family":"Molloy","sequence":"additional","affiliation":[{"name":"Computer Science, James Madison University , Harrisonburg, VA 22181, USA"},{"name":"School of Biology, James Madison University , Harrisonburg, VA 22181, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marc","family":"Vaisset","sequence":"additional","affiliation":[{"name":"LAAS-CNRS, Universit\u00e9 de Toulouse, CNRS , F-31400 Toulouse, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christophe","family":"Zanon","sequence":"additional","affiliation":[{"name":"LAAS-CNRS, Universit\u00e9 de Toulouse, CNRS , F-31400 Toulouse, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierre","family":"Fauret","sequence":"additional","affiliation":[{"name":"LAAS-CNRS, Universit\u00e9 de Toulouse, CNRS , F-31400 Toulouse, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thierry","family":"Sim\u00e9on","sequence":"additional","affiliation":[{"name":"LAAS-CNRS, Universit\u00e9 de Toulouse, CNRS , F-31400 Toulouse, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juan","family":"Cort\u00e9s","sequence":"additional","affiliation":[{"name":"LAAS-CNRS, Universit\u00e9 de Toulouse, CNRS , F-31400 Toulouse, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,8,25]]},"reference":[{"key":"2023020108413371200_btab584-B1","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1093\/bioinformatics\/btz684","article-title":"A reinforcement-learning-based approach to enhance exhaustive protein loop sampling","volume":"36","author":"Barozet","year":"2020","journal-title":"Bioinformatics"},{"key":"2023020108413371200_btab584-B2","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1002\/prot.26008","article-title":"Protein loops with multiple meta-stable conformations: a challenge for sampling and scoring methods","volume":"89","author":"Barozet","year":"2021","journal-title":"Proteins"},{"key":"2023020108413371200_btab584-B3","doi-asserted-by":"crossref","first-page":"E3416","DOI":"10.1073\/pnas.1711490115","article-title":"Exploring the structural origins of cryptic sites on proteins","volume":"115","author":"Beglov","year":"2018","journal-title":"Proc. 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